The high level of genetic diversity revealed with SSR’s may also contribute to the lack of correlation, as genetic similarity is lower with SSR’s than with other marker systems as seen in sugar cane using a range of markers types [21,22,16,23] and in other crops [31], which could reduce the statistical power to define relationships. This could be over come by the use of larger numbers of SSR’s. These results suggest that E. rockii is different to the other species studied. Successful crosses between E. rockii and sugar cane would introgress novel germplasm and assist in the broadening of the genetic base of sugar cane.